In the moments before the Cylon attack, Pegasus docked at the Scorpia Fleet Shipyards for a refit. The Command Navigation Program was disabled, and nonessential crewmen were allowed to disembark to see their families in a three month long extended shore-leave. A heavily-armed Cylon squadron jumped in range of the shipyards and fired nuclear missiles at it and the ships docked, destroying two Battlestars and three other ships in the opening minutes. Admiral Cain rushed to the CIC and ordered an immediate decoupling and blind jump to escape the combat area.[3][4]Pegasus found itself past the red line, four or five jumps away from its last position. Following the escape, a ship-wide assessment found some 723 crewmen had perished in the attack. Among its craft, twelve Vipers had been totally destroyed along with two Raptors, and a further seventeen undefined vehicles declared irreparable.[4]

When a Raptor reconnaissance mission sent to investigate the silence in com traffic confirmed the destruction of the colonies, Pegasus took part in a series of cavalry charges, jumping wherever Cylon forces were massing and engaging them before abandoning the area. Gina Inviere, a Cylon agent, manipulated Admiral Cain into jumping the ship into the vicinity of a Cylon staging post masquerading as a lightly-defended communications relay. Its Vipers were overwhelmed by fifteen squadrons of Raiders and suffered severe casualties. In the heat of the moment, the ship's Executive Officer, Colonel Belzen, refused an order to launch the reserve Vipers, protesting it as a suicide run. He was immediately executed by Admiral Cain, who made Colonel Fisk her new XO.[3][4]

Following the attack, Pegasus detected a small refugee fleet of civilian craft. Seeing the civilian fleet as a tactical risk, she instead had the ships cannibalised for spare parts and engineers impressed under threat of their families' murder by marines. The fifteen ships were quickly abandoned, lacking FTL capability to escape from any passing Cylon raiders.[3][4]

Several months after the Fall of the Twelve Colonies, Pegasus prepared for a major operation to cut off a Cylon fleet it had been shadowing. When it jumped ahead to stage an ambush, it instead made contact with a large civilian fleet protected by Galactica, an older Battlestar which had escaped destruction due to never being networked. Though there was initially much rejoice for the arrival of Pegasus, its reputation quickly began to sour. To the ire of President Roslin and the civilian population, Admiral Cain repeatedly failed to send equipment to the civilian ships, focusing only on resupplying Galactica. Problems also developed between Admiral Cain and Commander Adama over the re-assignment of senior officers for reasons directly relating to his personal command style, having failed to adequately punish officers such as Captains Adama and Thrace for infractions due to a crew shortage. Problems also emerged between Galactica's existing crew and those transferred from Pegasus, due to the revelations that a number of crew members had taken part in the systematic torture and rape of Gina. This dispute itself led to the killing of Lt. Alastair Thorne by Lt. Karl Agathon and Deck Chief Galen Tyrol as he prepared to rape a Cylon prisoner on Galactica. This incident resulted in the arrest of Lt. Agathon and Chief Tyrol, and their transfer to Pegasus pending execution. Commander Adama failed to persuade Admiral Cain to spare the men, scrambled Galactica's pilots to stage a rescue operation, leading to Pegasus launching its Vipers in response.[3] The stand-off ended when Lieutenant Starbuck reappeared from an unauthorized recon mission aboard the stealth Blackbird with photos of a mysterious Cylon ship being guarded by two Basestars. Interrogation of Pegasus' Cylon prisoner identified the mysterious ship as a "Resurrection Ship", wherein Raiders and Humanoid Cylons were downloaded into new bodies. Although Adama and Cain declare an uneasy truce in order to coordinate an attack on the Cylons, they make plans to assassinate each other, which was called off after the Resurrection Ship was destroyed. Admiral Cain, however, was soon after assassinated by Gina after escaping her cell.

In the aftermath of Cain's death, Commander Adama was promoted to the rank of Admiral by President Roslin, while Colonel Fisk was promoted to Commander and given command of Pegasus. During Fisk's command, officers on Pegasus became involved in the black market, and Fisk was able to gain influence due to his position, even going as far as to bribe Galactica's Colonel Tigh and Vice President Gaius Baltar with supplies. Soon after, however, Fisk was murdered by rival black marketeers, who were able to enter his quarters as guests. Following the death of Commander Fisk, Chief Engineer Barry Garner was given the new position. Commander Garner's own style of leadership caused new problems, as he developed megalomaniac and paranoid tendencies which frightened Pegasus' crew into total obedience. Against the advise of his XO, Major Adama, Garner ordered Pegasus to jump to a binary star system in search of a missing Raptor crew against Admiral Adama's orders. This turned out to be an ambush by Cylon forces, and Pegasus took heavy damage as a result, with Commander Garner dying after leaving CIC to perform maintenance only he was skilled enough to perform. Following Pegasus' return to the fleet, Major Adama was promoted to the rank of Commander.

As the first mission with its new commander, Pegasus was sent to search for a missing Raptor science team and came under attack from a force of First Cylon War era fighters. Pegasus was unable to leave due to problems with its FTL drive, but quickly fixed the problems and left, but not before Kara Thrace shot down an enemy fighter in the landing pod. Learning of the Guardians from Galactica's Cylon prisoner, "Sharon" and the First Hybrid, Admiral Adama accompanied Pegasus on the rescue mission. The mission was a success, with the Guardian Basestar and First Hybrid destroyed, but Pegasus' XO, Major Kendra Shaw, was killed.

In the weeks following the operation, the fleet discoverd a habitable world and began to colonize "New Caprica". Pegasus and Galactica, with skeleton crews, formed an orbital defense network over the new colony. However, when the colony was discovered a year later by a Cylon fleet they were forced to abandon the colony and jump away.

Pegasus is destroyed in action during the third-season episode "Exodus, Part 2". Disobeying orders from Admiral Adama to protect the civilians that first escape the Cylon occupation in the second season episode " Lay Down Your Burdens Part ll ", Apollo leaves all of his Viper squadrons with the civilian ships, along with most of the crew. Apollo is able to divert the attention of the four Cylon Basestars attacking Galactica after FTL jumping to New Caprica. The older battlestar continues to cover the evacuation of the New Caprica colonists. This distraction allows time for Galactica's FTL drives to be repaired and the planet-bound colonists to reach their ships and escape.

One Cylon Basestar is critically damaged by Pegasus' forward main batteries as it enters the fray, drawing the fire from the Basestars. After Galactica jumps away, Pegasus (now heavily damaged and unable to escape) is locked into a suicide course, weapons systems firing automatically. The crew is evacuated to several Raptors just before Pegasus rams a Basestar, destroying it. The explosion causes the battlestar to fragment, the starboard hangar pod colliding with and destroying another Basestar.